Variant report

Variant	rs2099938
Chromosome Location	chr6:161386772-161386773
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:161377508..161379938-chr6:161386154..161388991,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1123179	0.90[ASN][1000 genomes]
rs1123180	1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1123181	1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12175972	0.98[ASN][1000 genomes]
rs12661018	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13193780	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13195467	0.97[ASN][1000 genomes]
rs1536244	0.94[ASN][1000 genomes]
rs1814458	0.90[ASN][1000 genomes]
rs7760467	1.00[ASN][1000 genomes]
rs9346843	0.97[ASN][1000 genomes]
rs9347473	0.98[ASN][1000 genomes]
rs9347474	0.97[ASN][1000 genomes]
rs9347475	0.97[ASN][1000 genomes]
rs9355323	0.99[ASN][1000 genomes]
rs9355859	0.90[ASN][1000 genomes]
rs9355860	0.98[ASN][1000 genomes]
rs9364582	0.90[ASN][1000 genomes]
rs9364583	0.88[ASN][1000 genomes]
rs9365237	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9365238	0.98[ASN][1000 genomes]
rs9365239	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422347	chr6:161211171-161442377	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1030045	chr6:161359075-161562255	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv886817	chr6:161371621-161846654	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv3381361	chr6:161373617-161864101	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1023982	chr6:161382188-161549831	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2099938	TAGAP	cis	parietal	SCAN
rs2099938	TULP4	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161372800-161394000	Weak transcription	Right Atrium	heart
2	chr6:161382400-161389800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:161384200-161387200	Enhancers	Brain Germinal Matrix	brain
4	chr6:161384600-161386800	Enhancers	Fetal Brain Female	brain
5	chr6:161385600-161388600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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